Every time you select an aircraft on the Geoscape and right-click move it somewhere, the game unpauses. Could this behavior be modified so that holding Shift when right-click moving will queue up the move without unpausing the game?
It would help save ~precious game world seconds~ when I’m a few beers deep and forget to repause right after moving each aircraft (critical when trying to juggle planes to respond to fliers…)
Good. Next voice requesting that will definitely help. From what I know they are considering it as one of the options… But when it will be implemented… Who knows
This one is another old request for many. Definitely, go and add your vote to the petitions in the feedback tool asking for the same thing, and comment on it.
The good part, is that a mod already exists that changes this behavior. 
I seem to recall seeing a mod site where this was one of many mods that could be downloaded aNd installed.
In the next patch 1.13 that will come on October 1 together with DLC 4 we will give some options to player about this automatic unpausing. Not exactly what you are requesting but I think it will still help. There will be these options:
I’m thrilled this will be included. To clarify my original post, basically holding the Shift key would stop moving aircraft unpausing the game, but frankly the options you’re listing here are above and beyond my suggestion.
Well done. Thanks for paying attention to feedback.
Long time requested feature 
Good that they made even few options. My would be probably 3rd or 4th way to go.
And holding shift should still let you queue the route. Or it is no longer available?
EDIT: Oh, I see that geoscape manual waypoints were removed.